Appendix One

An Introduction To Brain Anatomy

Inevitably, in discussing how consciousness is produced by the brain, or what are termed the 'neural correlates of consciousness', i.e. what neural activity accompanies or generates consciousness, it is necessary to refer to different parts of the brain. By now, cognitive scientists have a substantial body of knowledge about the functions of different parts of the brain and how they interact with each other, although it is far from comprehensive, and subject to rapid change as research into neural functioning continues at an ever-increasing pace. The general reader will not normally have any detailed knowledge of brain anatomy, so in this book the use of anatomical terms has been kept to the minimum consistent with an adequate level of explanation; but even this minimum will be daunting to non-specialists. Here then is a list of those regions of the brain that are referred to in the book, characterizing their functions at a level of simplicity that will have experts curling their lips, and adding a brief note about the evolutionary emergence of each region. See also the Glossary.

It has to be constantly repeated that the existence of a particular feature or function in a modern-day animal proves little about the anatomy of that animal 600 million years ago, which is more or less when the brain first began to evolve. The direct knowledge that we have about the brain anatomy of ancient animals (our ancestors) is based partly on fossils, which consist mostly of hard tissue – the soft brain tissue has gone – but increasingly on DNA and mitochondrial analysis. While the succession of types of animal in our ancestral tree is reasonably secure, the assertions in the following sections about differentiation of the brain in early animals, even though based on generally accepted current levels of knowledge, are hardly better than informed guesswork, particularly as regards the functions of early divisions of the brain.

The Brain Stem

Pretty much everyone knows that the brain stem connects the spinal cord to the brain proper. It deals with highly instinctive survival functions including breathing, digestion, heart rate, and blood pressure; and controls many reflex motor responses. The brain stem includes the reticular formation, which is essential to consciousness and plays a major role in arousal (being awake and alert). The brain stem receives many types of sensory input and 'pre-processes' it before sending it on to higher parts of the human brain. The top section of the brain-stem is called the pons (bridge).

A primitive brain stem, termed a notochord, had already evolved about 600 million years ago (MYA) in our ancestors the Protostomes (modern-day example, the ragworm, see Chapter One), while longtitudinal nerve-cords existed in their own probable ancestor the Acoeli (flatworms), which are assumed to have had a fairly undifferentiated ganglion (collection of neural cells) towards the front part of the animal, and are the first known bilaterally symmetrical animals, although still invertebrate.

At a considerably later stage of brain evolution, the cerebellum (see below) developed alongside the pons. The brain-stem and the cerebellum are known together as the hind-brain.

The Three-Part Brain

The three-part brain consists of the fore-brain (prosencephalon), the mid-brain (mesencephalon) and the hind-brain (rhombencephalon). In early types of animal such as the ragworm, the fore-brain is chiefly concerned with the acquisition of food, using an olfactory sense, while the mid-brain processes optical input, perhaps mostly for reproductive purposes consequent upon particular external conditions of luminosity, and the hind-brain deals with control of motor activity.

The Fore-Brain

The ragworm already displays the three part arrangement of early animal brains, which was conserved to a considerable extent in subsequent brain evolution, and this arrangement is very clearly present in the hagfish, similar to our probable last pre-vertebrate ancestor (evolved c. 530 MYA, see Chapter One), and the lamprey (evolved c. 500 MYA), similar to probably our first vertebrate ancestor.

During embryonic development, in more advanced animals, the fore-brain divides into two sections, the cortex (telencephalon), destined to be the seat of intelligence and consciousness, and the set of regions dealing with emotion and other bodily drives (known as the diencephalon) as well as communication between the various brain regions.

The Mid-Brain

The evolutionary origins of the mid-brain, which sits on top of the pons at the head of the brain-stem and is known as the tectum (roof), are murky. The tectum consists of the superior colliculus and the inferior colliculus. It receives visual and auditory sensory input; in humans it is involved in only preliminary sensory processing, but in non-mammalian vertebrates it serves as the main visual area of the brain, functionally analogous to the visual areas of the cerebral cortex in mammals. It seems possible that in early animals, the eyes had a mostly reproductive function, judging the best moment for release of gametes based on prevailing light conditions (always in the sea, at that time, of course). It is thought that the visual sense thus evolved on top of the animal (dorsally) in distinction to the brain stem and spinal cord, which were originally underneath (ventral). Many writers suppose that during the period when Protostomes were evolving, the animal 'flipped over' (eg Telford, 2007) so that the nerve-cord moved to the top, and that may have been the moment at which the visually-oriented structures of the mid-brain joined up with the brain-stem (hind-brain).

The Diencephalon: Thalamus, Hypothalamus And Endocrine System

In modern animals with a cortex, the thalamus, which has a bi-lobed structure – the precursor of the two hemispheres of the developed mammal brain – is the gateway for all incoming sensory information on its way to the cortex. In early animals, such as the hagfish, which did not yet have a clearly defined cortex, such sensory integration as took place happened in or close to the thalamus, and it must also be the place where motor commands originated as a result. The hypothalamus, which is strongly connected to the thalamus and sits just underneath it (behind it, in the case of the eel-like hagfish) controls the endocrine system, the chemical messenger system of the body, which operates in conjunction with the electrical, neural messenger system. Chemical messengers are of course produced by glands, of which the pituitary gland, physically almost a part of the brain, was one of the earliest. The hagfish has (and is presumed to have had) a thalamus, a hypothalamus and a pituitary gland.

A diagram of the human brain showing how the thalamus sits on top of the brain-stem;
the tectum is labelled superior colliculus and inferior colliculus. 'Ventricle' means space, or void.

Copyright Eileen Nicole Simon;

Chemical messengers were and are a means of communicating affective (sometimes called hedonic) states to the body at large. In higher animals, the housing and implementation of affective states becomes a function of parts of the cortex (see below) and employs neural mechanisms as much as or more than chemical messengers; but in less developed animals affective agendas are a matter for the thalamus to deal with and are implemented mostly in chemical terms.

Even in modern versions of the hagfish and lamprey, there is relatively little communication between the several parts of the brain, although in both species there is a well-develope thalamus, and the fore-brain has acquired a new Extra Pyramidal System (EPS) that deals with involuntary motor commands, linked to an early version of the amygdala, permitting the expression of positive or negative haptic states (reward and avoidance) through motor activity. The EPS is so called because it came into existence before appearance of the system based on pryamidal neurons that underpins voluntary motor actions under the control of the cortex in more modern animals.


The cerebellum, which sits below the mid-brain at the top of the brain-stem, is mostly concerned with the fine control of movement, although it has been accredited with a number of other functions in higher mammals. While some cerebellar-like structures have been described in hagfish and lampreys, their role is disputed, and the consensus is that the cerebellum evolved first in post-lamprey vertebrates, after which it became universal in vertebrates, and has tended to become a proportionately larger part of the brain with advancing cortical sophistication. It receives input primarily from the brain-stem, and outputs mostly through the thalamus to the cortex.

The ability of the hagfish to tie itself into a knot and ease the knot up or down its length, assisted by its slimy surface, is the sort of wave-like succession of motor actions which might be thought to require a coordinating ability from the brain – just what the cerebellum evolved to provide; but if there is a cerebellum-like function in the hagfish brain, it is very undeveloped (Kusunoki et al, 1982).

The cerebellum in humans, as in all mammals, is a large body of closely packed neurons at the back of the brain stem with a highly individual structure, topographical in its lower regions (i.e. it maintains a map of the body).

It receives incoming sensory information, including proprioceptive information (feedback about the position of parts of the body) and is highly connected with the motor cortex (which eventually sends out motor commands to the muscles). See Nieuwenhuys (1967).

Motor activity, unless it is instinctive, is initiated by the cortex in higher animals: 'Let's run after that gazelle.' The cerebellum ensures the smoothness of movement on a time-scale of seconds by inhibiting motor impulses on a running time-base, feeding back information to the cortex.

The cerebellum has a role in memory formation, and specifically it helps to create categorizable mappings of smooth movement, which can be called on directly by the cortex in future. Once a set of such mappings exists the role of the cerebellum appears to diminish.


Human brain, showing the brain stem (Medulla oblongata and Pons) and Cerebellum.

From Gray's Anatomy (public domain)



This word is used to describe the 'fore-brain', whose main components are the cortex (cortical hemispheres), the amygdala, the hippocampus and the basal ganglia (whose most prominent component is the striatum). Very approximately, the functions of these components of the modern mammalian brain are as follows:

The Cortex The cortex (often called the neo-cortex, to distinguish it, perhaps unnecessarily, from the reptilian cortex) performs motor control, long-term planning, memory storage and generation of the 'remembered' or 'narrative' present.

Conventionally, the cortex is divided into lobes, which have differentiated functions. The frontal lobe, in particular, is understood to be the region in which advanced planning and analytical thinking take place.

In the picture opposite, the cerebellum appears to be directly connected with the cortex; but in reality the connections are made via the thalamus, whose role in the mammal brain is equivalent to that of a telephone exchange.

Human brain, showing how the cortex has expanded so as to envelop the earlier parts of the brain, which are thus hidden from view except from underneath. The cerebellum (see above) does not however form part of the cortex.

Reproduced under the terms of the Creative Commons Attribution-ShareAlike License.

The Amygdala The amygdala creates and maintains emotional states which can influence behaviour.

The Basal Ganglia The basal ganglia are involved in the construction and implementation of motor programs originated by the cortex, using input from regions of the brain concerned with choice, motivation and emotion. There are two of them; they are part of the forebrain, but can be thought of as being close to the midbrain

Information arriving in the basal ganglia from the cortex about impending or current motor programs can result in inhibitory impulses transmitted back to the cortex via the thalamus (Mumford, 1991). The role of the basal ganglia in the mediation of motor programs appears to have been conserved in the evolution of mammals from amphibians.

The Hippocampus The hippocampus is involved in the ordering of sequences of motor programs over timescales of seconds to minutes, something that is important in the operation of continuous short-term memory. Examples of sequences of motor activities that would involve the hippocampus might be, for a human, playing the piano or riding a bicyle, or for a snake, coiling or uncoiling, or slithering over a rock in its home territory. The same process also lays down the foundations of long-term memory.

Reproduced under the terms of the Creative Commons Attribution-ShareAlike License.
Provided by the US Food and Drug Administration.

The hippocampi are shown coloured pink; the view is from the underside of the cortex.

Reproduced under the terms of the Creative Commons Attribution-ShareAlike License.

The hypothalamus, amygdala, and hippocampus are together described as the limbic system, being associated with emotions such as fear and pleasure, memory, motivation, and various autonomic functions. The idea of a limbic 'system' as such has somewhat gone out of fashion, as it becomes apparent that the interconnections of the mammalian brain are too complex to permit of a separate system as such for affective or hedonic purposes.

Evolution Of The Modern Mammal Brain

Just as the mid-brain, with its visual function, probably evolved separately from the brain-stem (with its motor function) and joined up with it 550 million years ago, so it is supposed that the fore-brain, with its olfactory function, evolved separately and joined up with the mid-brain and hind-brain round about 500 million years ago. The olfactory sense probably evolved in connection with the detection of food, and some writers link the development of memory with the need for a data-base of information about the characteristics of food sources. Perhaps this idea gels with the power of smells to arouse very deep-seated and long-ago emotions.

The hagfish (from c. 530 MYA) is both invertebrate and jawless, and was succeeded by the lamprey (from c. 500 MYA), vertebrate but still jawless. These animals display increasing levels of connectivity between the various sections of the brain, and both have a primitive amygdala-striatum-hippocampus (diencephalon) linked to their olfactory sense. However it is then a big step forward to the next group of animals which can securely be tied back to our evolutionary tree, the Chondrichthians (eg the shark), which are jawed vertebrates and evolved about 460 MYA.

The emergence of jawed animals, probably between 480 and 500 million years ago, can perhaps be associated with greater differentiation of the parts of the fore-brain. By 450 million years ago, two types of jawed fish had emerged: plate-skinned archaic jawed fishes (cartilaginous fishes including sharks and rays) and bony jawed fishes (known as Placoderms). Although it's the latter that are in the direct line of our ancestry, the likelihood is that the two types had a common ancestor, and among existing fish it is probably the sharks that most closely rememble such an ancestor.

Although the mammalian brain is folded over on itself, making a ball, the sorts of long, marine animal which evolved during the period from 450-500 million years ago display the spatial succession of fore-brain/mid-brain/hind-brain very clearly. Fore-brain (to do with finding food and eating it) at the front, mid-brain (to do with eyes on the top of the head, initially more for reproductive purposes than for seeing prey) in the middle, and hind-brain (controlling the body via the spinal cord) at the back.

By the time that jawed fish had emerged, approximately 460 million years ago, this arrangement had become standard, and is well exemplified in the brain of the dogfish shark, shown below.

Sharks have very well developed olfactory lobes, a fore-brain with a thalamus, hypothalamus, pituitary gland, amygdala and a large pallium (forerunner of the cortex) with well-defined basal ganglia, although the hippocampus has not yet become differentiated.

There are two large optic lobes situated on top of the midbrain. The hind-brain has a well developed brainstem with a large cerebellum, sitting on top of the optic lobes in the picture on the left and obscuring the remainder of the mid-brain. The size of the cerebellum appears to vary along with the size of the pallium in different species.

There is great variation in the size of shark brains, altogether, associated with their different life-styles. Active, hunting sharks have larger brains (including larger cerebellums), while bottom-dwellers have smaller brains.

A drawing of a dorsal view of the brain of a dogfish shark, from the book
"The soul of man", by Paul Carus, 1905

About 430 million years ago, the lobe-finned fish (Sarcopterygians) evolved; these bony fish, with lobed, paired fins, are just about universally accepted as the ancestors of all tetrapods, i.e. four-limbed animals, which of course includes us humans, and their modern representatives, including the lung-fish and the famous coelacanth, which are thought to have conserved their original features to an unusual extent. The Sarcopterygians have rather small brains, but they exhibit all the features described above for the shark, and there is (disputed) evidence that the hippocampus has become differentiated.

In Amphibians, however, which evolved about 380 million years ago, there is no doubt that the hippocampus exists, although it is sometimes called the medial pallium (Gonzalez, 2002). As in so many other cases, the actual amphibian ancestor species has disappeared except in fossil form, but it is thought that its general plan has largely been conserved in modern amphibians, so that there is a fair degree of consensus on how the brain of the ancestral amphibian would have appeared.

The major divisions of the amphibian brain are essentially the same as in reptiles and mammals, although mammalian complexity is much greater, especially of course in the cortex (termed the dorsal pallium in amphibians and reptiles), which has a 6-layer construction in mammals rather than the 3-layer structure of the amphibian brain. There are however already a growing number of the re-entrant connections (feedback loops) which are such a marked feature of the mammalian brain. Herrick (The Brain of the Tiger Salamander) argues that these circuits serve to link the animal's internal motivations with its sensory and motor apparatus. One of the roles of these early additions to the simpler brains of the amphibians which preceded the Sauropsid ancestor is to mediate the interplay between emotions (already in existence through the amygdala) and what one can only call social behaviours, including cooperation, aggression, mating, rearing and teaching of young.

As compared with fish brains, the amphibian cortical hemispheres (dorsal pallium) have grown in importance and there is much more connectivity with the now very pronounced optical lobes of the mid-brain and directly with the brain-stem. On visual inspection, there appears to be far more integration between the olfactory bulbs of the fore-brain and the mid-brain; for the first time, the brain looks like one integrated body rather than separate bodies which have become connected.

A clearly differentiated cortex (still known as the pallium) makes its first appearance in the Sauropsids, a phylum which includes turtles, reptiles, lizards and birds. They are of course verterbrates (jellyfish and worms are invertebrates). It is not too clear what our original Sauropsid ancestor may have looked like, but it is a good guess that it appeared about 300 million years ago. Among extant Sauropsids, turtles are often said to be closest to the original ancestor, and snakes are quite remote.

With the evolution of reptiles the dorsal pallium grew in importance and size, reflecting the increased complexity of motor behaviour on dry land and the wealth of sensory information being delivered by expanded olfactory lobes. The part of the pallium known as the basal ganglia, and particularly the region called the striatum, developed a specialized role in the control of motor behaviour. The amygdala, hippocampus and basal ganglia, which had been linked in earlier animals, became more clearly differentiated, indeed separated by the growing pallium (Herrick, ibid; Carey, 1982).

It used to be thought that there were major structural differences between the mammalian and Sauropsid brains in terms of the cortex. It is fairly well accepted by now, however, that the mammalian neocortex and the equivalent Sauropsid (reptile) dorsal cortex and dorsal ventricular ridge (DVR) developed from a common antecedent, being the pallium, in the ancestor reptile that evolved from amphibians (eg Reiner, 2000; Husband and Shimizu, 2001). Recent research has show that functionally and biochemically there is a lot of similarity between mammalian and Sauropsid cortices. See Sanides (1969) and Deacon (1990).


Carey, J H (1982) Telencephalon of Reptiles, in Comparative Correlative Neuroanatomy of the Vertebrate Telencephalon, eds. Crosby, E C and Schnitzlein, H N, Macmillan, New York

Deacon, T W (1990) Rethinking Mammalian Brain Evolution, American Zoologist, 30, pp 629-705

Gonzalez, A and Lopez, J M (2002) A Forerunner of Septohippocampal Cholinergic System is Present in Amphibians, Neurosci Lett. 327(2), pp 111-114

Herrick, C J (1948) The Brain of the Tiger Salamander, University of Chicago Press, Chicago

Husband, S A and Shimizu, T (2001) Evolution of the Avian Visual System, in Avian Visual Cognition, ed. Cook, R,

Kusunoki, T, Kadota, T and Kishida, R (1982) Chemoarchitectonics of the Brain Stem of the Hagfish, Eptatretus Burgeri, with Special Reference to the Primordial Cerebellum, Hirnforsch., 23(1), pp 109-19

Loonen, A J M and Ivanova, S A (2015) Circuits Regulating Pleasure and Happiness: the Evolution of Reward-Seeking and Misery-Fleeing Behavioral Mechanisms in Vertebrates, Front Neurosci. 2015; 9: 394. Published online 2015 Oct 23. doi: 10.3389/fnins.2015.00394 PMCID: PMC4615821

Mumford, D (1991) On the Computational Architecture of the Neocortex: I. The Role of the Thalamo-Cortical Loop, Biological
Cybernetics, 65, pp 135-145

Nieuwenhuys, R (1967) Comparative Anatomy of the Cerebellum, Prog. Brain Res., 25, pp 1–93

Reiner, A J (2000) A Hypothesis as to the Organization of Cerebral Cortex in the Common Amniote Ancestor of Modern Reptiles and Mammals, Evolutionary Developmental Biology of the Cerebral Cortex, No. 228, Novartis Foundation

Reiner, A, Yamamoto, K and Karten, H J (2005) Organization and Evolution of the Avian Forebrain, The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 287A(1), pp 1080-1102

Sanides, F (1969) Comparative Architectonics of the Neocortex of Mammals and Their Evolutionary Interpretation, Annals of the New York Academy of Sciences, 167, pp 404-423

Telford, M J (2007) A Single Origin of the Central Nervous System? Cell, 129(2), pp 237-239


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